5 ms·

Same vibe as "I would just simply..." What do you think the entire medical, pharmaceutical, bioinformatic, etc. industries have been doing for decades? Are you

Same vibe as "I would just simply..." What do you think the entire medical, pharmaceutical, bioinformatic, etc. industries have been doing for decades? Are you really so arrogant to think that other people are too lazy and stupid to think of your brilliant idea and that you are simply more intelligent than everybody else? Do you really think people haven't been trying?

function_seven 5y ago
If they aren't mass collecting this data in the first place (for the reasons outlined above), then how can they be doing this? Or, if they are doing this from quality samples of the population, then we have data to show that, for example, "Yes, Mr. Function Seven, your scan shows elevated levels of Widget-5a enzymes. This is often a precursor to Gadget Cancer, but 30% of the population shows this elevation, while only 1% develop the cancer. It's best to do nothing at this time unless we see further elevation. Have a good day, see you next year" So either we have this data and we can give accurate advice, or we don't have this data because we're afraid of over-diagnosing non-problems. I understand the fear, but it's still burying one's head in the sand to not even look.
- rackjack 5y ago
  They are mass collecting the data. They have more data than they know what to do with. Bioinformatics abuses data science at levels comparable to Google and Facebook. They are getting quality samples from the population. But it's not a simple as "high enzyme = maybe good chance of cancer". How are you going to get those enzymes from their blood in a way that can be applied to the general population? Before that, how do you know there's not confounding factors (of which they are a LOT)? > So either we have this data and we can give accurate advice, or we don't have this data because we're afraid of over-diagnosing non-problems. It's not that easy. Look at this pathway: https://www.pathwaycommons.org/guide/workflows/rna_seq_to_enrichment_map/identify_pathways/figure_idpathways_il5_netpath_diagram.png https://www.pathwaycommons.org/guide/workflows/rna_seq_to_en... From here: https://www.pathwaycommons.org/guide/workflows/rna_seq_to_enrichment_map/identify_pathways/ https://www.pathwaycommons.org/guide/workflows/rna_seq_to_en... This is what people think the activation of genes is. What they THINK the activation of genes is. Note the following: - They don't know all the genes. They are constantly identifying new ones. The number of gene pathways people are pretty sure are complete is small. I don't know if this one is one of the "pretty sure" ones. - Gene pathways are not just complex in terms of size, they are also non-linear. This is not a computer program, this is a horrible biological mess where biological components constantly and probabilistically emit chemicals. I don't even think that the pathway I gave you is super representative - it doesn't feature the ridiculous non-linearity and uncertainty that many pathways at the bleeding edge have. They can get much worse. People are not burying their heads in the sand. They are trying their almighty to dig up from bedrock and reach the sky.
  - jghn 5y ago
    > Bioinformatics abuses data science at levels comparable to Google and Facebook. To give people a sense of this, it is not unheard of for large scale bioinformatics platforms to set off alarms and/or zone-level capacity issues with the large cloud providers.
  - hebrox 5y ago
    Would you say that they could collect way more data?
avion23 5y ago
> Are you really so arrogant to think that other people are too lazy and stupid to think of your brilliant idea and that you are simply more intelligent than everybody else? Not OP, but yes, I do. I've had some runins with the health system. At least the parts that I've seen are worse than the dark ages. Especially endocrinologists have absolutely no clue what they are doing. The ones I met don't even have superficial knowledge about their full-time job which they've performed for ~20 years. And yes, this sounds arrogant. I've tripple checked whether I'm just tripping. Their knowledge is not simply outdated, but never correct to begin with. I think it's a cultural problem which shows in a lot of areas. Medicine doesn't value human life as much as f.e. air transport
- rackjack 5y ago
  You're talking about praxis, we're talking about research. I agree the praxis can be pretty bad, but in regards to the above commenter's remarks on why people don't just simply collect data and apply it, medical professionals simply cannot try out new treatments the way they are suggesting.
  - jghn 5y ago
    To go further, a large issue/distraction in biomedical research has been Big Tech types coming in assuming that the roadblock all along has been lack of smart computational people in the process. I will not name names, but have seen so many instances of personal tech heroes coming in & claiming the underlying problem was that some of the brightest computational I've ever encountered simply didn't know how to computer. Nothing could be further from the truth. People coming in to "disrupt" only add noise. Eventually those people either understand this and put the effort in to understand the domain or they wander off.
    - Robotbeat 5y ago
      While it’s absolutely true that naive non-experts can end up adding a lot more heat than light, I’ve also seen non-expert people come into stagnant domains and absolutely completely transform and improve upon the state of the art. I am skeptical of the “more data is bad” meme of screening hesitancy. It cannot be scientifically true in the strictest sense, and to the degree it’s an accurate assertion, it really seems to reveal an unscientificness to how screening data is used today in practice rather than that in principle more data is bad.
deeviant 5y ago
> Are you really so arrogant to think that other people are too lazy and stupid to think of your brilliant idea and that you are simply more intelligent than everybody else? Do you really think people haven't been trying? I find it hard to believe I'm reading this sentiment on HN. Do you realize nearly any disruptive idea has do the "arrogant" thing you are speaking off. Big companies go out of business all the time, industry disappear or wane all the time, big companies/industries with lots of smart people do stupid stuff on the regular. Characterizing the desire to do something other than status quo as "arrogance" is just the bottom of the barrel. I'm glad Semmelweis didn't think the way you do.
- jjeaff 5y ago
  I didn't understand their comment to mean that at all. It's not arrogant to think there might be a better way. It probably is arrogant to think that the better way is actually really simple and easy to implement. Arrogance definitely can play a big role in success of many startup entrepreneurs. Because they think the answer is simple and their arrogance shields them from not trying. So they go down the road and find out the solution is actually quite complicated, but a small percentage succeed in accomplishing the goal. But it's still arrogance, nonetheless.
epicureanideal 5y ago
> What do you think the entire medical, pharmaceutical, bioinformatic, etc. industries have been doing for decades? Well, let's remember that the AlphaFold team at Google solved the protein folding problem with a relatively small team in a relatively small number of years after extremely large, well funded companies whose primary business was drug development failed to do so for decades. So yeah, it's been demonstrated to be possible that the current leaders in a field might be significantly less capable than a different team.
- timy2shoes 5y ago
  > let's remember that the AlphaFold team at Google solved the protein folding problem with a relatively small team in a relatively small number of years after extremely large, well funded companies whose primary business was drug development failed to do so for decades Did they though? They did extremely well at CASP14, and much better than competing groups. But does this solve protein folding? Deepmind's marketing department would have you think so, but for those of us that work in the field we know that this is not the case. Furthermore, does protein folding solve the relevant problems of drug design? It solve the forward problem, given an amino acid sequence predict its 3d structure. But for drug design we need the inverse problem, given a specified structure predict an amino acid sequence that produces that structure.
- wxnx 5y ago
  There's confounding here that you're ignoring. For reference, I'm a machine learning research scientist who started in bioinformatics, initially lured by the possibility of a machine learning solution to the protein folding problem. Google's research arm has made leaps and bounds in a particular field (deep learning) and then managed to apply it successfully to a very, very hard problem (protein folding). That other companies failed to adapt Google's successes in deep learning faster than Google is not surprising at all to me. One might argue that the impact of academic-big pharma collaboration (in the form of funding for research projects related to CASP) is what enabled a company like Google, with no independent desire to collect the massive amounts of wetlab data required to evaluate or develop a tool like AlphaFold, to even participate. More importantly, AlphaFold hasn't really solved the protein folding problem well enough for drug development. So, the entire debate might be moot.
kilotaras 5y ago
> Are you really so arrogant to think that other people are too lazy and stupid to think of your brilliant idea and that you are simply more intelligent than everybody else? Here's a report of a person whose wife had seasonal affective disorder. He - deduced that a powerful enough lightbox should be able to cure SAD - didn't find any examples of such treatments in literature - spent $600 to build "LUMINATOR" - "And as of early 2017, with two winters come and gone, Brienne seems to no longer have crippling SAD—though it took a lot of light bulbs, including light bulbs in her bedroom that had to be timed to go on at 7:30am before she woke up, to sustain the apparent cure." https://www.lesswrong.com/posts/zsG9yKcriht2doRhM/inadequacy-and-modesty#iv_ https://www.lesswrong.com/posts/zsG9yKcriht2doRhM/inadequacy...

function_seven 5y ago

If they aren't mass collecting this data in the first place (for the reasons outlined above), then how can they be doing this? Or, if they are doing this from quality samples of the population, then we have data to show that, for example, "Yes, Mr. Function Seven, your scan shows elevated levels of Widget-5a enzymes. This is often a precursor to Gadget Cancer, but 30% of the population shows this elevation, while only 1% develop the cancer. It's best to do nothing at this time unless we see further elevation. Have a good day, see you next year" So either we have this data and we can give accurate advice, or we don't have this data because we're afraid of over-diagnosing non-problems. I understand the fear, but it's still burying one's head in the sand to not even look.

rackjack 5y ago
They are mass collecting the data. They have more data than they know what to do with. Bioinformatics abuses data science at levels comparable to Google and Facebook. They are getting quality samples from the population. But it's not a simple as "high enzyme = maybe good chance of cancer". How are you going to get those enzymes from their blood in a way that can be applied to the general population? Before that, how do you know there's not confounding factors (of which they are a LOT)? > So either we have this data and we can give accurate advice, or we don't have this data because we're afraid of over-diagnosing non-problems. It's not that easy. Look at this pathway: https://www.pathwaycommons.org/guide/workflows/rna_seq_to_enrichment_map/identify_pathways/figure_idpathways_il5_netpath_diagram.png https://www.pathwaycommons.org/guide/workflows/rna_seq_to_en... From here: https://www.pathwaycommons.org/guide/workflows/rna_seq_to_enrichment_map/identify_pathways/ https://www.pathwaycommons.org/guide/workflows/rna_seq_to_en... This is what people think the activation of genes is. What they THINK the activation of genes is. Note the following: - They don't know all the genes. They are constantly identifying new ones. The number of gene pathways people are pretty sure are complete is small. I don't know if this one is one of the "pretty sure" ones. - Gene pathways are not just complex in terms of size, they are also non-linear. This is not a computer program, this is a horrible biological mess where biological components constantly and probabilistically emit chemicals. I don't even think that the pathway I gave you is super representative - it doesn't feature the ridiculous non-linearity and uncertainty that many pathways at the bleeding edge have. They can get much worse. People are not burying their heads in the sand. They are trying their almighty to dig up from bedrock and reach the sky.
- jghn 5y ago
  > Bioinformatics abuses data science at levels comparable to Google and Facebook. To give people a sense of this, it is not unheard of for large scale bioinformatics platforms to set off alarms and/or zone-level capacity issues with the large cloud providers.
- hebrox 5y ago
  Would you say that they could collect way more data?

avion23 5y ago

> Are you really so arrogant to think that other people are too lazy and stupid to think of your brilliant idea and that you are simply more intelligent than everybody else? Not OP, but yes, I do. I've had some runins with the health system. At least the parts that I've seen are worse than the dark ages. Especially endocrinologists have absolutely no clue what they are doing. The ones I met don't even have superficial knowledge about their full-time job which they've performed for ~20 years. And yes, this sounds arrogant. I've tripple checked whether I'm just tripping. Their knowledge is not simply outdated, but never correct to begin with. I think it's a cultural problem which shows in a lot of areas. Medicine doesn't value human life as much as f.e. air transport

rackjack 5y ago
You're talking about praxis, we're talking about research. I agree the praxis can be pretty bad, but in regards to the above commenter's remarks on why people don't just simply collect data and apply it, medical professionals simply cannot try out new treatments the way they are suggesting.
- jghn 5y ago
  To go further, a large issue/distraction in biomedical research has been Big Tech types coming in assuming that the roadblock all along has been lack of smart computational people in the process. I will not name names, but have seen so many instances of personal tech heroes coming in & claiming the underlying problem was that some of the brightest computational I've ever encountered simply didn't know how to computer. Nothing could be further from the truth. People coming in to "disrupt" only add noise. Eventually those people either understand this and put the effort in to understand the domain or they wander off.
  - Robotbeat 5y ago
    While it’s absolutely true that naive non-experts can end up adding a lot more heat than light, I’ve also seen non-expert people come into stagnant domains and absolutely completely transform and improve upon the state of the art. I am skeptical of the “more data is bad” meme of screening hesitancy. It cannot be scientifically true in the strictest sense, and to the degree it’s an accurate assertion, it really seems to reveal an unscientificness to how screening data is used today in practice rather than that in principle more data is bad.

deeviant 5y ago

> Are you really so arrogant to think that other people are too lazy and stupid to think of your brilliant idea and that you are simply more intelligent than everybody else? Do you really think people haven't been trying? I find it hard to believe I'm reading this sentiment on HN. Do you realize nearly any disruptive idea has do the "arrogant" thing you are speaking off. Big companies go out of business all the time, industry disappear or wane all the time, big companies/industries with lots of smart people do stupid stuff on the regular. Characterizing the desire to do something other than status quo as "arrogance" is just the bottom of the barrel. I'm glad Semmelweis didn't think the way you do.

jjeaff 5y ago
I didn't understand their comment to mean that at all. It's not arrogant to think there might be a better way. It probably is arrogant to think that the better way is actually really simple and easy to implement. Arrogance definitely can play a big role in success of many startup entrepreneurs. Because they think the answer is simple and their arrogance shields them from not trying. So they go down the road and find out the solution is actually quite complicated, but a small percentage succeed in accomplishing the goal. But it's still arrogance, nonetheless.

epicureanideal 5y ago

> What do you think the entire medical, pharmaceutical, bioinformatic, etc. industries have been doing for decades? Well, let's remember that the AlphaFold team at Google solved the protein folding problem with a relatively small team in a relatively small number of years after extremely large, well funded companies whose primary business was drug development failed to do so for decades. So yeah, it's been demonstrated to be possible that the current leaders in a field might be significantly less capable than a different team.

timy2shoes 5y ago
> let's remember that the AlphaFold team at Google solved the protein folding problem with a relatively small team in a relatively small number of years after extremely large, well funded companies whose primary business was drug development failed to do so for decades Did they though? They did extremely well at CASP14, and much better than competing groups. But does this solve protein folding? Deepmind's marketing department would have you think so, but for those of us that work in the field we know that this is not the case. Furthermore, does protein folding solve the relevant problems of drug design? It solve the forward problem, given an amino acid sequence predict its 3d structure. But for drug design we need the inverse problem, given a specified structure predict an amino acid sequence that produces that structure.
wxnx 5y ago
There's confounding here that you're ignoring. For reference, I'm a machine learning research scientist who started in bioinformatics, initially lured by the possibility of a machine learning solution to the protein folding problem. Google's research arm has made leaps and bounds in a particular field (deep learning) and then managed to apply it successfully to a very, very hard problem (protein folding). That other companies failed to adapt Google's successes in deep learning faster than Google is not surprising at all to me. One might argue that the impact of academic-big pharma collaboration (in the form of funding for research projects related to CASP) is what enabled a company like Google, with no independent desire to collect the massive amounts of wetlab data required to evaluate or develop a tool like AlphaFold, to even participate. More importantly, AlphaFold hasn't really solved the protein folding problem well enough for drug development. So, the entire debate might be moot.

kilotaras 5y ago

> Are you really so arrogant to think that other people are too lazy and stupid to think of your brilliant idea and that you are simply more intelligent than everybody else? Here's a report of a person whose wife had seasonal affective disorder. He - deduced that a powerful enough lightbox should be able to cure SAD - didn't find any examples of such treatments in literature - spent $600 to build "LUMINATOR" - "And as of early 2017, with two winters come and gone, Brienne seems to no longer have crippling SAD—though it took a lot of light bulbs, including light bulbs in her bedroom that had to be timed to go on at 7:30am before she woke up, to sustain the apparent cure." https://www.lesswrong.com/posts/zsG9yKcriht2doRhM/inadequacy-and-modesty#iv_ https://www.lesswrong.com/posts/zsG9yKcriht2doRhM/inadequacy...